Biowulf High Performance Computing at the NIH
RMBlast on Biowulf

RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ rmblastn
[user@cn3144 ~]$  
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. rmblast.sh). For example:

#!/bin/sh
set -e
module load rmblast
rmblastn -query query.fasta -subject reference.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] rmblast.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. rmblast.swarm). For example:

rmblastn -query query01.fasta -subject reference.fasta
rmblastn -query query02.fasta -subject reference.fasta
rmblastn -query query03.fasta -subject reference.fasta
rmblastn -query query04.fasta -subject reference.fasta

Submit this job using the swarm command.

swarm -f rmblast.swarm [-g #] [-t #] --module rmblast
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module rmblast Loads the rmblast module for each subjob in the swarm